TSS identification and sequence retrieve

[Qichen Yuan]

Hi UCSC Genome Browser staff:

I am wondering how could I easily pinpoint the TSS of an endogenous gene through the UCSC genome browser? Although I can use SwitchGear TSS, it is quite hard to copy the DNA information surrounding the TSS annotated by this track, could you suggest a convenient way to find the TSS information, including the local DNA context surrounding the TSS?

Best, Qichen

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

You can use the Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables, to download the transcription start site (TSS) sequence with the DNA sequence surrounding the annotation. Using the following settings on the Table Browser, you can get the TSS with 100 bp upstream and downstream the annotation:

Step 1: Configure the Table Browser

On Table Browser, apply the following settings.

clade: mammal
genome: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Regulation
track: SwitchGear TSS
table: switchDbTss
region: genome
output format: sequence

Step 2: Get output

Once the track is selected, click the get output button. You will then be taken to a new page where you can add 100 bp upstream and downstream for each item. After setting the formatting options. Click 'get sequence'.

I wanted to also mention that the SwitchGear TSS track was last updated in 2010. You might want to use the Track Search feature (Genome Browser --> Track Search) to find other TSS tracks available on hg19, https://genome.ucsc.edu/cgi-bin/hgTracks?hgt_tSearch=track+search.

An engineer shares that the EPDnew Promoters track, https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=epdNew, might be of interest to you. The mailing list archive is useful to learn how to get TSS for other tracks. For example, here is a previously answered question about getting the TSS from the UCSC Genes track, https://groups.google.com/a/soe.ucsc.edu/g/genome/c/jsQrDjY_GGw/m/CCFTZyPsBwAJ.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genome Browser

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